PetrusBotha:
When connecting an Xbee I realized that the analog Read values are pushed up quite a lot, normal quiet environment reads will be in the range of 500 to 600, with the Xbee they are pushed to 900 or more. Is it an issue with power distribution or something affecting the RX/TX ports on the Arduino?
Probably RF noise intruding on your analog circuitry. To test this, temporarily replace the microphones with resistors (or switch them off, if they are switchable) then check your values with and without Xbee.
Attention to your analog ground path could help here, as might using sheilded cable to connect the mics if you aren't already. Also, capacitive low-pass filtering to get rid of high frequency hash may help.